Distribution and restricted vertical movement of nematodes in a heavy clay soil

A large part of Australia’s broad acre irrigation industry, which includes cotton, is farmed on heavy clay Vertosols. Recent changes in nematicide chemical availability, changes in rotations and the observation of the reniform nematode in central Queensland has highlighted that we need to improve our understanding of nematodes in these soils. We undertook preliminary investigations into distribution by depth under a cotton-cotton and cotton-maize rotation as well as vertical movement experiments in microcosms to better understand nematode distribution and movement in heavy clay soils. Analysis revealed that field populations decreased with soil sample depth, but there were also differences between rotations. In microcosm experiments, vertical movement of nematodes in these heavy clay soils was restricted, even in the presence of plant roots and moisture, both of which were hypothesised to improve nematode migration. The results imply that crop rotation currently remains a plausible option for nematode control, and that we still have a lot to learn about the ecology of nematode populations in Vertosols

The serotype distribution among healthy carriers before vaccination is essential for predicting the impact of pneumococcal conjugate vaccine on invasive disease.

Pneumococcal conjugate vaccines (PCVs) have substantially reduced morbidity and mortality of pneumococcal disease. The impact of the 7-valent PCV on all-serotype invasive pneumococcal disease (IPD) among children was reported to vary between high-income countries. We investigate the ability to predict this heterogeneity from pre-vaccination data. We propose a parsimonious model that predicts the impact of PCVs from the odds of vaccine serotype (VT) among carriers and IPD cases in the pre-PCV period, assuming that VT are eliminated in a mature PCV programme, that full serotype replacement occurs in carriage and that invasiveness of the NVT group is unchanged. We test model performance against the reported impact of PCV7 on childhood IPD in high-income countries from a recent meta-analysis. The odds of pre-PCV7 VT IPD, PCV schedule, PCV coverage and whether a catch up campaign was used for introduction was gathered from the same analysis. We conducted a literature review and meta-analysis to obtain the odds of pre-PCV7 VT carriage in the respective settings. The model predicted the reported impact on childhood IPD of mature PCV programmes; the ratio of predicted and observed incidence risk ratios was close to 1 in all settings. In the high income settings studied differences in schedule, coverage, and catch up campaigns were not associated with the observed heterogeneity in impact of PCV7 on childhood all-serotype IPD. The pre-PCV7 proportion of VT IPD alone also had limited predictive value. The pre-PCV7 proportion of VT carriage and IPD are the main determinants for the impact of PCV7 on childhood IPD and can be combined in a simple model to provide predictions of the vaccine preventable burden of IPD

Subsoil Microbial Diversity and Stability in Rotational Cotton Systems

Microbial diversity has been well documented for the top 0-0.30 m of agricultural soils. However, spatio-temporal research into subsoil microbial diversity and the effects of agricultural management remains limited. Soil type may influence subsoil microbial diversity, particularly Vertosols. These soils lack distinct horizons and are known to facilitate the downward movement of organic matter, potentially supporting subsoil microbiota, removed from the crop root system (i.e., bulk soils). Our research used the MiSeq Illumina Platform to investigate microbial diversity down the profile of an agricultural Australian Vertosol to 1.0 m in bulk soils, as influenced by crop system (continuous cotton and cotton-maize) and sample time (pre- and in-crop samples collected over two seasons). Overall, both alpha- (Chao1, Gini-Simpson Diversity and Evenness indices) and beta-diversity (nMDS and Sørensen's Index of Similarity) metrics indicated that both bacterial (16S) diversity and fungal (ITS) diversity decreased with increasing soil depth. The addition of a maize rotation did not significantly influence alpha-diversity metrics until 0.70-1.0 m depth in the soil, where bacterial diversity was significantly higher in this system, with beta-diversity measures indicating this is likely due to root system differences influencing dissolved organic carbon. Sample time did not significantly affect bacterial or fungal diversity over the two seasons, regardless of the crop type and status (i.e., crop in ground and post crop). The relatively stable subsoil fungal and overall microbial diversity in bulk soils over two crop seasons suggests that these microbiota have developed a tolerance to prolonged agricultural management

Assessing the efficiency of catch-up campaigns for the introduction of pneumococcal conjugate vaccine: a modelling study based on data from PCV10 introduction in Kilifi, Kenya.

BACKGROUND: The World Health Organisation recommends the use of catch-up campaigns as part of the introduction of pneumococcal conjugate vaccines (PCVs) to accelerate herd protection and hence PCV impact. The value of a catch-up campaign is a trade-off between the costs of vaccinating additional age groups and the benefit of additional direct and indirect protection. There is a paucity of observational data, particularly from low- and middle-income countries, to quantify the optimal breadth of such catch-up campaigns. METHODS: In Kilifi, Kenya, PCV10 was introduced in 2011 using the three-dose Expanded Programme on Immunisation infant schedule and a catch-up campaign in children <5 years old. We fitted a transmission dynamic model to detailed local data, including nasopharyngeal carriage and invasive pneumococcal disease (IPD), to infer the marginal impact of the PCV catch-up campaign over hypothetical routine cohort vaccination in that setting and to estimate the likely impact of alternative campaigns and their dose efficiency. RESULTS: We estimated that, within 10 years of introduction, the catch-up campaign among children <5 years old prevents an additional 65 (48-84) IPD cases across age groups, compared to PCV cohort introduction alone. Vaccination without any catch-up campaign prevented 155 (121-193) IPD cases and used 1321 (1058-1698) PCV doses per IPD case prevented. In the years after implementation, the PCV programme gradually accrues herd protection, and hence its dose efficiency increases: 10 years after the start of cohort vaccination alone the programme used 910 (732-1184) doses per IPD case averted. We estimated that a two-dose catch-up among children <1 year old uses an additional 910 (732-1184) doses per additional IPD case averted. Furthermore, by extending a single-dose catch-up campaign to children aged 1 to <2 years and subsequently to those aged 2 to <5 years, the campaign uses an additional 412 (296-606) and 543 (403-763) doses per additional IPD case averted. These results were not sensitive to vaccine coverage, serotype competition, the duration of vaccine protection or the relative protection of infants. CONCLUSIONS: We find that catch-up campaigns are a highly dose-efficient way to accelerate population protection against pneumococcal disease

Subsoil Microbial Processes Under Australian Rotational Cotton Systems

Soil microbiota have been well characterised in agricultural topsoils (0 - 30 cm depth) globally. However, understanding of microbial functioning below 30 cm is in its infancy, particularly in the Southern Hemisphere. Increasing pressure on developing sustainable agricultural practices has instigated a shift to investigating subsoil (&gt;30 cm depth) microbial dynamics. In the Australian cotton industry, interest in subsoils has increased due to the physical properties of Vertosol soils, on which most Australian cotton is grown. Commonly referred to as 'cracking clays', Vertosols have the unique characteristics of self-mulching and cracks extending well below the topsoil. These properties, along with frequent irrigations, are thought to facilitate the movement of organic matter and other nutrients, into deeper soil horizons and hypothesised to be utilised by subsoil microbiota.30 cm depth) microbial dynamics. In the Australian cotton industry, interest in subsoils has increased due to the physical properties of Vertosol soils, on which most Australian cotton is grown. Commonly referred to as 'cracking clays', Vertosols have the unique characteristics of self-mulching and cracks extending well below the topsoil. These properties, along with frequent irrigations, are thought to facilitate the movement of organic matter and other nutrients, into deeper soil horizons and hypothesised to be utilised by subsoil microbiota. This project represents an initial study into microbial processes down the soil profile (0 – 100 cm) under cotton crops grown in Vertosols at the Australian Cotton Research Institute (ACRI), New South Wales. The overarching PhD aims were to i) Evaluate the potential for subsoil microbial activity to perform ecosystem services and ii) Determine the influence of crop rotation (continuous cotton and cotton-maize rotations) and sample time (3 sample points over two cropping seasons) on subsoil microbial processes. Microbial activity and biomass were assessed by respiration and stable oxygen isotope methodologies, whilst microbial diversity was measured utilising high throughput sequencing. Microbial biomass and diversity analyses followed the expected trend of decreasing measurements with increasing depth, following the trends observed in international studies. Microbial activity was just as prevalent in subsoils for both field fresh and long-term (isotopic) assessments, which has not been observed in other studies. A lack of significant differences in microbial processes down the soil profiles under continuous cotton and cotton-maize systems was also observed. This research has led us to believe that the physical properties of Vertosols (self-mulching and formation of deep cracks) facilitate microbial activity in subsoils, thus having the potential to contribute to ecosystem services. It would also appear that the physical properties of Vertosols exert a greater influence than system management

Subsoil microbial processes under Australian rotational cotton systems

This collection pertains to the data collected for the purpose of PhD research, under Research Project UNE1601. Data is organised in line with thesis entitled "Subsoil microbial processes under Australian rotational cotton systems" - for example, data relating to Chapter 2, is organised in folders under this heading and with file names indicating thesis sections. Data includes both raw and analysed sets, most of which are in excel spreadsheets. Metagenomic data has a range of file types, however the raw data can be accessed through CSV or excel file types. Data were collected at the Australian Cotton Research Institute, New South Wales, Australia

Subsoil Microbial Diversity and Stability in Rotational Cotton Systems

Microbial diversity has been well documented for the top 0–0.30 m of agricultural soils. However, spatio-temporal research into subsoil microbial diversity and the effects of agricultural management remains limited. Soil type may influence subsoil microbial diversity, particularly Vertosols. These soils lack distinct horizons and are known to facilitate the downward movement of organic matter, potentially supporting subsoil microbiota, removed from the crop root system (i.e., bulk soils). Our research used the MiSeq Illumina Platform to investigate microbial diversity down the profile of an agricultural Australian Vertosol to 1.0 m in bulk soils, as influenced by crop system (continuous cotton and cotton–maize) and sample time (pre- and in-crop samples collected over two seasons). Overall, both alpha- (Chao1, Gini–Simpson Diversity and Evenness indices) and beta-diversity (nMDS and Sørensen’s Index of Similarity) metrics indicated that both bacterial (16S) diversity and fungal (ITS) diversity decreased with increasing soil depth. The addition of a maize rotation did not significantly influence alpha-diversity metrics until 0.70–1.0 m depth in the soil, where bacterial diversity was significantly higher in this system, with beta-diversity measures indicating this is likely due to root system differences influencing dissolved organic carbon. Sample time did not significantly affect bacterial or fungal diversity over the two seasons, regardless of the crop type and status (i.e., crop in ground and post crop). The relatively stable subsoil fungal and overall microbial diversity in bulk soils over two crop seasons suggests that these microbiota have developed a tolerance to prolonged agricultural management

Do you lube before you probe?

Climate change is a real concern for most of us on this planet and, as most of us know, agriculture has a part to play. Whether it's due to the loss of soil organic matter as carbon dioxide (CO2) as a result of cultivation or the flush of nitrous oxide (N2O) as nitrogenous fertilisers are reduced under flooded soils, there's a chunk of the human contribution to this issue that lays at farmers' feet. But it's not as though we're doing nothing to better understand and mitigate these potentially harmful agricultural practices, which are widely recognised as being important components in continuing high yield crop production to feed and clothe the ever growing global population

Coring lubricants can increase soil microbial activity in Vertisols

It is essential that sampling procedures for biological measurements are done in a way that reflects the soil processes, whilst limiting sampling artefacts. In heavy clay Vertisol soils, coring lubricants are often considered necessary in order to extract and recover soil for quality and health assessments. Previous reports into the use of coring lubricants have found soil carbon measurements to be inflated but to date, a study to evaluate the effects of these lubricants on soil microbial activity, has not been forthcoming. We measured soil carbon dioxide (CO2) evolution in response to the addition of common coring lubricants, to determine the effects upon soil microbial activity to the depth of 100 cm. Application of coring lubricants to the surface soil layers of field collected cores did not significantly influence CO2 evolution however, microbial activity increased in deeper soil layers (30–100 cm) with the use of WD-40, mould stripper and silicone oil. When the ratio of coring lubricant to soil was increased to ~5 g coring lubricant to 100 g−1 soil, there was a significant (P = .001) effect on microbial activity, with silicone oil and mould stripper inflating measurements by at least 5%, whilst olive oil and WD-40 were similar to the control. The results imply that when using coring rigs to recover soil for microbial functional analysis in Vertisols, the use of coring lubricants is best avoided, with further research recommended